Low alignment rates of synthetic reads to gold standard coassembly scaffolds

[shw079]

Hi, I don't know if this is the right place to talk about this, but I am using the 2nd CAMI Challenge Human Microbiome Project Toy Dataset. When I mapped the reads (bowtie2) to the gold standard co-assembly scaffolds, for oral, skin, and airways, the alignment rate is pretty high (>99%), but for gastrointestinal tract and urogenital tract, the alignment rate is very low (~40%). I am wondering why this is happening for these two body sites. Thanks!

[AlphaSquad]

Interesting, thanks for pointing this out. Could you point us to the exact files you used for mapping so we can reproduce this and investigate what might be going on?

[shw079]

I just used the anonymous_reads.fq in Illumina synthetic samples. For gastrointestinal tract and urogenital tract, the alignment rates are low for all samples. I trimmed and filtered the reads and redid the alignment again, which improved the alignment rates but they are still low.

For example, after trimming, for 2017.12.04_18.56.22_sample_6 in urogenital tract, the alignment rate is only ~15%.

[AlphaSquad]

We are investigating this. It is possible that the gold standards for urogenital and gastrointestinal tract are mixed up with each other.

[AlphaSquad]

Could you please post/send via email the exact steps/commands you performed?
The tests I did so far could not reproduce this problem, i.e. the read file short_read/2017.12.04_18.56.22_sample_6/reads/anonymous_reads.fq.gz had a 100% mapping rate to the hybrid/pooled/anonymous_gsa.fasta

[shw079]

I have short_read/2017.12.04_18.56.22_sample_6/reads/anonymous_reads.fq.gz mapped to short_read/gsa.fasta.gz and I haven't touched hybrid/pooled/anonymous_gsa.fasta. Is that the problem?

[AlphaSquad]

I tried reproducing this, exact steps follow:
Downloading the reads from sample 6 with
java -jar camiClient.jar -d https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/CAMI_Urogenital_tract . sample_6/reads/anonymous_reads then downloading the corresponding gsa with java -jar camiClient.jar -d https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/CAMI_Urogenital_tract . short_read/gsa, then unzipping and mapping with gunzip gsa.fasta.gz and gunzip anonymous_reads.fq.gz, bwa index gsa.fasta, bwa mem gsa.fasta anonymous_reads.fq > gsa.sam, samtools view -bS gsa.sam > gsa.bam and finally samtools flagstat gsa.bam and got a mapping rate of 100%.
Maybe you accidentally overwrote the urogenital/gastrointestinal gold standards when downloading the next set? Anyhow, I will add a new Issue about unique filenames based on the sample name.

[abremges]

This seems resolved; else please let us know and we'll re-open the issue and further look into it.
I support the idea proposed in #39 for a next version, maybe already for CAMI2 data generation.